Science, people used to say, is the simple pursuit of knowledge. But this is no longer true. Commercial interests are taking over our universities, and intense economic and political pressures are put on scientists to pursue research that offers raw economic results.

Nowhere is this more apparent than within the GM debate, where any scientist who confronts the GM juggernaut is sure to be vilified and have their reputation ruined if they dare speak about their research before a "peer review" in a scientific journal.

Peer review is the safety net that guards science - research submitted to a journal is checked by peers to guarantee it is credible before publication. But while some kind of checking system is needed - and peer review can work - no system is foolproof. Some scientists complain that, in practice, peer review stops critical science being disseminated.

Last week the Royal Society, Britain's oldest scientific establishment, launched an investigation into how the results of scientific research are published. It will be looking closely at the case of GM, and has set up a working party to investigate whether peer review provides the establishment with a means to prevent unorthodox ideas from being made public.

But already this investigation looks like it will be used to attack those who have published science critical of commercially sensitive areas - as evidenced in an interview with a member of the working party, Professor Paul Harvey, in the Scotsman. The working party is dominated by royal fellows and their supporters - of the 14 people on it, only one is a consumer representative.

One subject of the Scotsman attack was Dr Arpad Pusztai, who appeared on World in Action in 1998 concerned with the health effects of GM. With decades of research and 270 scientific papers to his name, he was hardly a charlatan. But he spoke before his work had appeared in a peer-reviewed journal and the establishment castigated him. He was suspended, gagged for months, and his research team was disbanded. But he stands by his results, parts of which were later published in the Lancet. Pusztai said of the scientific establishment at the time: "Their remit was to screw me and they screwed me."

A recent review in the journal Nutrition and Health found only 10 published studies into the health risks of GM and noted that five of these were "in collaboration" with private companies with no adverse effects reported. Four of the others were by Dr Pusztai; all showed "adverse effects".

Pusztai is not alone in being vilified. Ignacio Chapela and David Quist found GM contamination in Mexican maize and published their work in Nature. They too were hounded, forcing Nature to issue a bodged retraction. "I don't want to be a martyr," Dr Chapela told me, "but I cannot avoid now realising that this is a very, very well-concerted and coordinated and paid-for campaign to discredit the very simple statement we made."

Chapela has since faced a campaign to deny him tenure as a microbiologist at the University of Berkeley. Quist and Chapela are also likely to get roasted during the Royal Society investigation, although they too stand by their work.

The scientific establishment's obsession with the "peer review" means important science that raises risks of GM technology is side-lined. Two of the GM sceptics on the recent science review panel of the GM debate were Professor Carlo Leifert, from the Tesco Centre for Organic Agriculture and Dr Andrew Stirling from Sussex University. Leifert resigned partly because he feared that staying would jeopardise his application for a major EU grant; but also because the panel only looked at peer- reviewed science and ignored the majority of critical science into GM.

But other scientists complain of far worse. Dr Stirling is an expert on risk assessment at the science policy research unit. Because of his sceptical position, a senior pro-GM scientist tried to sabotage his career, rubbishing his work and trying to get him dropped from a research project. "Such behaviour by individuals in privileged academic or regulatory positions threatened seriously to compromise the credibility and proper functioning of the science advice system," note the minutes of the science review panel.

Such behaviour undermines the process of science and sends a chilling message to any scientist just starting out: keep your head down and don't dare to question. What is happening to critical GM scientists is evocative of what happened to those critical of nuclear power, toxic pollution, BSE and foot and mouth.

Dr Pat Costner is a senior scientist with Greenpeace. In the early 90s, Costner's home and office were burned down in an arson attack, a month before she was to publish results of a investigation into toxic waste incineration. "I used to love the silence," said Costner. "Now it haunts me." As critical voices in the GM debate get attacked, the sound of silence should haunt us all.

· Andy Rowell is author of Don't Worry It Is Safe to Eat, published by Earthscan.